Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 11:27:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d74_27227/08_2023/8d74_27227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d74_27227/08_2023/8d74_27227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d74_27227/08_2023/8d74_27227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d74_27227/08_2023/8d74_27227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d74_27227/08_2023/8d74_27227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d74_27227/08_2023/8d74_27227.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 6150 2.51 5 N 1611 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ASP 497": "OD1" <-> "OD2" Residue "B TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 532": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 9639 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain: "D" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1416 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1607 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 20, 'TRANS': 178} Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3197 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 378} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.36, per 1000 atoms: 0.56 Number of scatterers: 9639 At special positions: 0 Unit cell: (97.75, 141.95, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1843 8.00 N 1611 7.00 C 6150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 390 " " NAG A 703 " - " ASN A 157 " " NAG A 704 " - " ASN A 383 " " NAG A 705 " - " ASN A 379 " " NAG C 401 " - " ASN C 142 " " NAG E 1 " - " ASN A 227 " " NAG F 1 " - " ASN C 190 " " NAG G 1 " - " ASN B 407 " " NAG H 1 " - " ASN B 426 " " NAG I 1 " - " ASN B 303 " " NAG J 1 " - " ASN B 243 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 24 sheets defined 13.3% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.843A pdb=" N SER A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.534A pdb=" N ASN A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 43 removed outlier: 4.367A pdb=" N LEU D 16 " --> pdb=" O HIS D 12 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 97 Processing helix chain 'D' and resid 102 through 130 removed outlier: 3.621A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 183 removed outlier: 4.032A pdb=" N GLU D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.926A pdb=" N VAL B 163 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.732A pdb=" N CYS B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 214 " --> pdb=" O LEU B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 214' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 8.237A pdb=" N LYS A 221 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.253A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 205 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.253A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.038A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.645A pdb=" N ARG A 300 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 removed outlier: 3.672A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.129A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 403 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 367 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 399 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 371 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.109A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.109A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 117 Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 211 through 214 Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 258 Processing sheet with id=AB7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AB8, first strand: chain 'B' and resid 141 through 147 removed outlier: 3.968A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 156 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 157 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B 201 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.544A pdb=" N TYR B 223 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 173 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.518A pdb=" N CYS B 270 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 262 removed outlier: 6.313A pdb=" N LYS B 259 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 330 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 261 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 279 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 337 through 342 removed outlier: 5.180A pdb=" N GLN B 338 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN B 354 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.580A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.938A pdb=" N HIS B 454 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE B 439 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER B 452 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 464 through 471 removed outlier: 3.884A pdb=" N ILE B 484 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS B 466 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 482 " --> pdb=" O CYS B 466 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG B 480 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 470 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 478 " --> pdb=" O ILE B 470 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3033 1.35 - 1.48: 2598 1.48 - 1.60: 4219 1.60 - 1.73: 0 1.73 - 1.85: 47 Bond restraints: 9897 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 9892 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 496 107.47 - 114.09: 5801 114.09 - 120.72: 3407 120.72 - 127.35: 3626 127.35 - 133.98: 164 Bond angle restraints: 13494 Sorted by residual: angle pdb=" C TRP A 164 " pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.46e+00 angle pdb=" N CYS B 511 " pdb=" CA CYS B 511 " pdb=" C CYS B 511 " ideal model delta sigma weight residual 108.96 112.97 -4.01 1.49e+00 4.50e-01 7.25e+00 angle pdb=" C TYR B 502 " pdb=" N THR B 503 " pdb=" CA THR B 503 " ideal model delta sigma weight residual 121.54 125.92 -4.38 1.91e+00 2.74e-01 5.27e+00 angle pdb=" C CYS B 511 " pdb=" N SER B 512 " pdb=" CA SER B 512 " ideal model delta sigma weight residual 122.16 125.15 -2.99 1.32e+00 5.74e-01 5.12e+00 angle pdb=" CA LEU B 184 " pdb=" CB LEU B 184 " pdb=" CG LEU B 184 " ideal model delta sigma weight residual 116.30 124.16 -7.86 3.50e+00 8.16e-02 5.04e+00 ... (remaining 13489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5305 17.09 - 34.17: 381 34.17 - 51.26: 65 51.26 - 68.35: 13 68.35 - 85.43: 10 Dihedral angle restraints: 5774 sinusoidal: 2335 harmonic: 3439 Sorted by residual: dihedral pdb=" CA THR B 447 " pdb=" C THR B 447 " pdb=" N ALA B 448 " pdb=" CA ALA B 448 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS B 466 " pdb=" SG CYS B 466 " pdb=" SG CYS B 511 " pdb=" CB CYS B 511 " ideal model delta sinusoidal sigma weight residual 93.00 63.50 29.50 1 1.00e+01 1.00e-02 1.24e+01 dihedral pdb=" CA HIS D 97 " pdb=" C HIS D 97 " pdb=" N PHE D 98 " pdb=" CA PHE D 98 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1282 0.052 - 0.103: 219 0.103 - 0.155: 56 0.155 - 0.206: 5 0.206 - 0.258: 1 Chirality restraints: 1563 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 426 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 131 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 142 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1560 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 501 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 445 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 446 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 446 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 446 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 337 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 338 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.017 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 494 2.73 - 3.27: 8975 3.27 - 3.81: 14828 3.81 - 4.36: 16953 4.36 - 4.90: 30339 Nonbonded interactions: 71589 Sorted by model distance: nonbonded pdb=" OG1 THR A 341 " pdb=" O TYR A 344 " model vdw 2.184 2.440 nonbonded pdb=" O LEU A 364 " pdb=" O3 NAG A 704 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR B 409 " pdb=" O7 NAG G 1 " model vdw 2.230 2.440 nonbonded pdb=" O GLY B 283 " pdb=" OG1 THR B 285 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR A 371 " pdb=" O LEU A 397 " model vdw 2.309 2.440 ... (remaining 71584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.920 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9897 Z= 0.173 Angle : 0.507 7.858 13494 Z= 0.256 Chirality : 0.043 0.258 1563 Planarity : 0.004 0.066 1679 Dihedral : 12.344 85.432 3510 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1153 helix: 1.82 (0.39), residues: 127 sheet: -1.67 (0.23), residues: 420 loop : -2.99 (0.20), residues: 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.143 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 145 average time/residue: 0.2781 time to fit residues: 53.2982 Evaluate side-chains 99 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0887 time to fit residues: 2.7603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS A 485 ASN D 12 HIS D 42 GLN D 76 ASN D 107 GLN D 122 GLN D 145 ASN D 163 GLN D 182 HIS ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 255 GLN C 256 HIS B 166 HIS B 226 ASN B 313 ASN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN B 403 GLN B 458 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 9897 Z= 0.331 Angle : 0.664 7.878 13494 Z= 0.339 Chirality : 0.050 0.281 1563 Planarity : 0.005 0.065 1679 Dihedral : 4.301 19.045 1247 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.23), residues: 1153 helix: 2.33 (0.41), residues: 134 sheet: -1.37 (0.23), residues: 438 loop : -2.37 (0.22), residues: 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.001 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 125 average time/residue: 0.2239 time to fit residues: 39.4877 Evaluate side-chains 111 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0890 time to fit residues: 5.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 9897 Z= 0.273 Angle : 0.595 11.702 13494 Z= 0.302 Chirality : 0.047 0.218 1563 Planarity : 0.004 0.062 1679 Dihedral : 4.438 19.823 1247 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1153 helix: 2.51 (0.42), residues: 135 sheet: -1.17 (0.23), residues: 450 loop : -2.26 (0.23), residues: 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.129 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 121 average time/residue: 0.2645 time to fit residues: 44.7453 Evaluate side-chains 96 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0911 time to fit residues: 3.4805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 29 optimal weight: 0.0670 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9897 Z= 0.167 Angle : 0.575 12.323 13494 Z= 0.284 Chirality : 0.045 0.214 1563 Planarity : 0.004 0.062 1679 Dihedral : 4.304 19.264 1247 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.24), residues: 1153 helix: 2.90 (0.42), residues: 134 sheet: -0.87 (0.24), residues: 441 loop : -2.16 (0.23), residues: 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 0.2350 time to fit residues: 35.1259 Evaluate side-chains 98 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0903 time to fit residues: 4.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 226 HIS C 139 ASN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 9897 Z= 0.436 Angle : 0.713 8.385 13494 Z= 0.363 Chirality : 0.052 0.301 1563 Planarity : 0.005 0.062 1679 Dihedral : 5.162 20.759 1247 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.85 % Favored : 91.07 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1153 helix: 2.15 (0.42), residues: 135 sheet: -1.20 (0.23), residues: 468 loop : -2.20 (0.23), residues: 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 119 average time/residue: 0.2160 time to fit residues: 36.3669 Evaluate side-chains 105 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0901 time to fit residues: 5.0121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9897 Z= 0.184 Angle : 0.564 7.354 13494 Z= 0.286 Chirality : 0.045 0.229 1563 Planarity : 0.004 0.059 1679 Dihedral : 4.746 21.704 1247 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1153 helix: 2.73 (0.43), residues: 134 sheet: -0.98 (0.24), residues: 468 loop : -2.11 (0.24), residues: 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 1.126 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 0.2199 time to fit residues: 32.5353 Evaluate side-chains 97 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0959 time to fit residues: 3.7570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 92 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9897 Z= 0.160 Angle : 0.586 15.496 13494 Z= 0.289 Chirality : 0.053 1.056 1563 Planarity : 0.004 0.060 1679 Dihedral : 4.688 34.267 1247 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.24), residues: 1153 helix: 2.87 (0.43), residues: 134 sheet: -0.81 (0.24), residues: 457 loop : -2.05 (0.24), residues: 562 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.098 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.2280 time to fit residues: 31.8418 Evaluate side-chains 89 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0886 time to fit residues: 2.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9897 Z= 0.168 Angle : 0.621 25.590 13494 Z= 0.298 Chirality : 0.061 1.536 1563 Planarity : 0.004 0.059 1679 Dihedral : 4.663 33.473 1247 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.24), residues: 1153 helix: 2.94 (0.42), residues: 134 sheet: -0.82 (0.24), residues: 454 loop : -1.95 (0.24), residues: 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.217 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 93 average time/residue: 0.2323 time to fit residues: 31.1189 Evaluate side-chains 86 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0932 time to fit residues: 2.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 9897 Z= 0.410 Angle : 0.727 15.174 13494 Z= 0.366 Chirality : 0.063 1.444 1563 Planarity : 0.005 0.058 1679 Dihedral : 5.309 31.188 1247 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.93 % Favored : 90.98 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1153 helix: 2.28 (0.42), residues: 134 sheet: -1.12 (0.24), residues: 461 loop : -2.04 (0.24), residues: 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.150 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.2595 time to fit residues: 35.7118 Evaluate side-chains 94 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0892 time to fit residues: 2.7009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9897 Z= 0.194 Angle : 0.615 12.837 13494 Z= 0.306 Chirality : 0.054 1.036 1563 Planarity : 0.004 0.055 1679 Dihedral : 5.005 29.490 1247 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1153 helix: 2.69 (0.43), residues: 134 sheet: -0.97 (0.24), residues: 452 loop : -1.94 (0.24), residues: 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.068 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.2560 time to fit residues: 33.1763 Evaluate side-chains 87 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0901 time to fit residues: 1.7656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.0970 chunk 37 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127032 restraints weight = 13469.949| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.42 r_work: 0.3566 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9897 Z= 0.178 Angle : 0.591 9.758 13494 Z= 0.294 Chirality : 0.050 0.784 1563 Planarity : 0.004 0.056 1679 Dihedral : 4.851 28.549 1247 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.81 % Favored : 92.11 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1153 helix: 2.81 (0.43), residues: 134 sheet: -0.89 (0.24), residues: 453 loop : -1.89 (0.24), residues: 566 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.84 seconds wall clock time: 46 minutes 18.82 seconds (2778.82 seconds total)